R SIG Debian - May 2009 - [Fwd: Re: ubuntu problem with 'r-cran-robustbase' [FWD Agustin Lobo]]

Subject: Re: [R-sig-Debian] ubuntu problem with 'r-cran-robustbase' [FWD
Agustin Lobo]
Date: Tue, 12 May 2009 13:30:49 +0200
From: Agustin Lobo <aloboaleu at gmail.com>
Reply-To: aloboaleu at gmail.com
To: Dirk Eddelbuettel <edd at debian.org>
CC: Martin Maechler <maechler at stat.math.ethz.ch>,
R-SIG-Debian at stat.math.ethz.ch
References: <18953.17704.527898.355877 at lynne.math.ethz.ch>
<18953.23458.954016.424944 at ron.nulle.part>

Dirk,
> So on Ubuntu, uninstall r-cran-robustbase and re-install robustbase 
from CRAN
> sources.  And file a bug report with Ubuntu.
That's the first thing I did: tried to install using
install.packages("robustbase"), which downloads the source and tries
to
compile. But the gcc step fails:
gcc -std=gnu99 -shared -o robustbase.so R-rng4ftn.o init.o lmrob.o mc.o
qn_sn.o rf-common.o rffastmcd.o rfltsreg.o wgt_himed.o -L/usr/lib/R/lib
-lRlapack -lblas -L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran -lm
-L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran -lm -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -lRlapack
collect2: ld returned 1 exit status

Also, when you say "fill a bug with Ubuntu", is there an r-sig-ubuntu
or
the Launchpad for general bug reports in Ubuntu?

Thanks

Agus


Dirk Eddelbuettel escribi?:
> On 12 May 2009 at 11:45, Martin Maechler wrote:
> | Agustin, posted on R-help.
> | I think the problem is one of the debian/ubuntu package
> | 'r-cran-robustbase' and its setup or (missing?) dependencies.
> | 
> | I can confirm Agustin's problem, working on Ubuntu 8.04.2
> | (8.04 is a "LTS" = long time support version).
> | 
> |   apt-get install r-cran-robustbase
> | 
> | works fine, but when trying to load the package,
> | there's a DLL - dependency on libRlapack.so 
> | which is not fulfilled (and not fulfillable: There's *no*
> | libRlapack.so).
> | 
> | For me,
> | 
> |   $ /usr/bin/R CMD config LAPACK_LIBS
> |   -llapack
> | 
> | and lapack.so is found inside /usr/lib/R/modules/ 
> | and liblapack.so from the 'lapack3' Debian/Ubuntu package 
> | is simply in /usr/lib/libpack.so  
> | 
> | Could it be that this is caused by an Ubuntu / Debian 
> | mismatch?
> 
> Scratch Debian here. It works there:
> 
> edd at ron:~> echo 'library(robustbase);cat("Hi\n")' |
R --silent --no-save
> R> library(robustbase);cat("Hi\n")
> Hi
> R>
> edd at ron:~>
> 
> It looks like Ubuntu failed to rebuild the package. The Rlapack.so vs
> lapack.so is an old one from the Atlas 3.6 / gfortran transition well over
a
> year ago and had affected other package.
> 
> So on Ubuntu, uninstall r-cran-robustbase and re-install robustbase from
CRAN
> sources.  And file a bug report with Ubuntu.
> 
> Dirk
> 
> 
> | Thank you in advance,
> | 
> | Martin Maechler, ETH Zurich
> | 
> | ------- start of forwarded message -------
> | From: Agustin Lobo <aloboaleu at gmail.com>
> | To: "r-help at r-project.org" <r-help at r-project.org>
> | Subject: [R] robustbase: cannot install
> | Date: Mon, 11 May 2009 18:20:14 +0200
> | 
> | This is really odd,
> | I've installed the binary of robustbase through synaptic on an ubuntu
> | 8.04 machine and get:
> |  > library(robustbase)
> | Error in dyn.load(file, DLLpath = DLLpath, ...) :
> |    unable to load shared library 
> | '/usr/lib/R/site-library/robustbase/libs/robustbase.so':
> |    libRlapack.so: cannot open shared object file: No such file or
directory
> | Error: package/namespace load failed for 'robustbase'
> |  >
> | 
> | The package is where it is suposed to be:
> | /usr/lib/R/site-library/robustbase
> | 
> | is this not a problem at compiling?
> | 
> | The problem is that if I try to install the source with 
> | install.packages("robustbase"), I get:
> | gcc -std=gnu99 -shared -o robustbase.so R-rng4ftn.o init.o lmrob.o mc.o 
> | qn_sn.o rf-common.o rffastmcd.o rfltsreg.o wgt_himed.o -L/usr/lib/R/lib 
> | -lRlapack -lblas -L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran -lm 
> | -L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran -lm -L/usr/lib/R/lib -lR
> | /usr/bin/ld: cannot find -lRlapack
> | collect2: ld returned 1 exit status
> | 
> | Despite the fact that I do have Rlapack:
> | ~$ R CMD config LAPACK_LIBS
> | -L/usr/lib/R/lib -lRlapack
> | 
> | Am I doing something wrong?
> | 
> | Thanks
> | 
> | Agus
> | -- 
> | Dr. Agustin Lobo
> | Institut de Ciencies de la Terra "Jaume Almera" (CSIC)
> | LLuis Sole Sabaris s/n
> | 08028 Barcelona
> | Spain
> | Tel. 34 934095410
> | Fax. 34 934110012
> | email: Agustin.Lobo at ija.csic.es
> | http://www.ija.csic.es/gt/obster
> | 
> | ______________________________________________
> | R-help at r-project.org mailing list
> | https://stat.ethz.ch/mailman/listinfo/r-help
> | PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> | and provide commented, minimal, self-contained, reproducible code.
> | ------- end of forwarded message -------
> | 
> | _______________________________________________
> | R-SIG-Debian mailing list
> | R-SIG-Debian at r-project.org
> | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
>

Agus,

robustbase just installed fine on my stock 8.04 system.  Please make 
sure that you have added all the repositories and packages suggested on 
this page:

http://cran.r-project.org/bin/linux/ubuntu/

Backports are important, and make sure you have r-base-dev
installed.  You may also need to be root (via sudo) to install, although 
there are instructions for local installation.  You can run the 
following commands to see what R related packages you have installed.

dpkg --get-selections | grep r-base
dpkg --get-selections | grep r-cran

Michael

Agustin Lobo wrote:
> Subject: Re: [R-sig-Debian] ubuntu problem with 'r-cran-robustbase'
[FWD
> Agustin Lobo]
> Date: Tue, 12 May 2009 13:30:49 +0200
> From: Agustin Lobo <aloboaleu at gmail.com>
> Reply-To: aloboaleu at gmail.com
> To: Dirk Eddelbuettel <edd at debian.org>
> CC: Martin Maechler <maechler at stat.math.ethz.ch>,
> R-SIG-Debian at stat.math.ethz.ch
> References: <18953.17704.527898.355877 at lynne.math.ethz.ch>
> <18953.23458.954016.424944 at ron.nulle.part>
> 
> Dirk,
>> So on Ubuntu, uninstall r-cran-robustbase and re-install robustbase 
> from CRAN
>> sources.  And file a bug report with Ubuntu.
> 
> That's the first thing I did: tried to install using
> install.packages("robustbase"), which downloads the source and
tries to
> compile. But the gcc step fails:
> gcc -std=gnu99 -shared -o robustbase.so R-rng4ftn.o init.o lmrob.o mc.o
> qn_sn.o rf-common.o rffastmcd.o rfltsreg.o wgt_himed.o -L/usr/lib/R/lib
> -lRlapack -lblas -L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran -lm
> -L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran -lm -L/usr/lib/R/lib -lR
> /usr/bin/ld: cannot find -lRlapack
> collect2: ld returned 1 exit status
> 
> Also, when you say "fill a bug with Ubuntu", is there an
r-sig-ubuntu or
> the Launchpad for general bug reports in Ubuntu?
> 
> Thanks
> 
> Agus
> 
> 
> Dirk Eddelbuettel escribi?:
>> On 12 May 2009 at 11:45, Martin Maechler wrote:
>> | Agustin, posted on R-help.
>> | I think the problem is one of the debian/ubuntu package
>> | 'r-cran-robustbase' and its setup or (missing?) dependencies.
>> | | I can confirm Agustin's problem, working on Ubuntu 8.04.2
>> | (8.04 is a "LTS" = long time support version).
>> | |   apt-get install r-cran-robustbase
>> | | works fine, but when trying to load the package,
>> | there's a DLL - dependency on libRlapack.so | which is not
fulfilled
>> (and not fulfillable: There's *no*
>> | libRlapack.so).
>> | | For me,
>> | |   $ /usr/bin/R CMD config LAPACK_LIBS
>> |   -llapack
>> | | and lapack.so is found inside /usr/lib/R/modules/ | and 
>> liblapack.so from the 'lapack3' Debian/Ubuntu package | is
simply in
>> /usr/lib/libpack.so  | | Could it be that this is caused by an Ubuntu 
>> / Debian | mismatch?
>>
>> Scratch Debian here. It works there:
>>
>> edd at ron:~> echo
'library(robustbase);cat("Hi\n")' | R --silent --no-save
>> R> library(robustbase);cat("Hi\n")
>> Hi
>> R>
>> edd at ron:~>
>>
>> It looks like Ubuntu failed to rebuild the package. The Rlapack.so vs
>> lapack.so is an old one from the Atlas 3.6 / gfortran transition well 
>> over a
>> year ago and had affected other package.
>>
>> So on Ubuntu, uninstall r-cran-robustbase and re-install robustbase 
>> from CRAN
>> sources.  And file a bug report with Ubuntu.
>>
>> Dirk
>>
>>
>> | Thank you in advance,
>> | | Martin Maechler, ETH Zurich
>> | | ------- start of forwarded message -------
>> | From: Agustin Lobo <aloboaleu at gmail.com>
>> | To: "r-help at r-project.org" <r-help at
r-project.org>
>> | Subject: [R] robustbase: cannot install
>> | Date: Mon, 11 May 2009 18:20:14 +0200
>> | | This is really odd,
>> | I've installed the binary of robustbase through synaptic on an 
>> ubuntu | 8.04 machine and get:
>> |  > library(robustbase)
>> | Error in dyn.load(file, DLLpath = DLLpath, ...) :
>> |    unable to load shared library | 
>> '/usr/lib/R/site-library/robustbase/libs/robustbase.so':
>> |    libRlapack.so: cannot open shared object file: No such file or 
>> directory
>> | Error: package/namespace load failed for 'robustbase'
>> |  >
>> | | The package is where it is suposed to be:
>> | /usr/lib/R/site-library/robustbase
>> | | is this not a problem at compiling?
>> | | The problem is that if I try to install the source with | 
>> install.packages("robustbase"), I get:
>> | gcc -std=gnu99 -shared -o robustbase.so R-rng4ftn.o init.o lmrob.o 
>> mc.o | qn_sn.o rf-common.o rffastmcd.o rfltsreg.o wgt_himed.o 
>> -L/usr/lib/R/lib | -lRlapack -lblas -L/usr/lib/gcc/i486-linux-gnu/4.2 
>> -lgfortran -lm | -L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran -lm 
>> -L/usr/lib/R/lib -lR
>> | /usr/bin/ld: cannot find -lRlapack
>> | collect2: ld returned 1 exit status
>> | | Despite the fact that I do have Rlapack:
>> | ~$ R CMD config LAPACK_LIBS
>> | -L/usr/lib/R/lib -lRlapack
>> | | Am I doing something wrong?
>> | | Thanks
>> | | Agus
>> | -- | Dr. Agustin Lobo
>> | Institut de Ciencies de la Terra "Jaume Almera" (CSIC)
>> | LLuis Sole Sabaris s/n
>> | 08028 Barcelona
>> | Spain
>> | Tel. 34 934095410
>> | Fax. 34 934110012
>> | email: Agustin.Lobo at ija.csic.es
>> | http://www.ija.csic.es/gt/obster
>> | | ______________________________________________
>> | R-help at r-project.org mailing list
>> | https://stat.ethz.ch/mailman/listinfo/r-help
>> | PLEASE do read the posting guide 
>> http://www.R-project.org/posting-guide.html
>> | and provide commented, minimal, self-contained, reproducible code.
>> | ------- end of forwarded message -------
>> | | _______________________________________________
>> | R-SIG-Debian mailing list
>> | R-SIG-Debian at r-project.org
>> | https://stat.ethz.ch/mailman/listinfo/r-sig-debian
>>
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian
-- 
Dr. Michael A. Rutter
School of Science
Penn State Erie, The Behrend College
Station Road
Erie, PA 16563
http://math.bd.psu.edu/faculty/rutter

Good (but astonishing) news:
1. (As noted in previous message)
After having removed r-base-core and
installed back r-base and r-base-dev
the binary installation of robustbase
apt-get install r-cran-robustbase

still gives in R the same error as before:
> require(robustbase)
Loading required package: robustbase
Error in dyn.load(file, DLLpath = DLLpath, ...) :
   unable to load shared library
'/usr/lib/R/site-library/robustbase/libs/robustbase.so':
   libRlapack.so: cannot open shared object file: No such file or directory

2. After removing the binary
apt-get remove r-cran-robustbase

The source installation using install.packages("robustbase") from
within
R works fine. The gcc step now works using lapack:

gcc -std=gnu99 -shared -o robustbase.so R-rng4ftn.o init.o lmrob.o mc.o
qn_sn.o rf-common.o rffastmcd.o rfltsreg.o wgt_himed.o -llapack -lblas
-lgfortran -lm -lgfortran -lm -L/usr/lib/R/lib -lR

Thank you all.

Agus


Michael Rutter wrote:
> Once you have reinstalled the packages, you should re-install robustbase.
> 
> sudo R
> install.packages("robustbase")
> 
> If at that point it fails, I'm not sure what can be done.  It would
seem
> you system has a flaw and a re-install would be best.  Jaunty (9.04) 
> installs very quickly and works great.  I would give that a try.
> 
> Michael
> 
> Agustin Lobo wrote:
>> No. What I have is what is listed in
>> http://cran.r-project.org/bin/linux/ubuntu/
>>
>> deb http://<my.favorite.cran.mirror>/bin/linux/ubuntu hardy/
>>
>> which in my case is
>>
>> deb http://cran.r-project.org/bin/linux/ubuntu hardy/
>>
>> Should I include the one you suggest? Should I replace the one
>> I have with this one?
>>
>> Agus
>>
>> Michael Rutter wrote:
>>> Agus,
>>>
>>> Do you have this in your sources list:
>>>
>>> deb http://lib.stat.cmu.edu/R/CRAN/bin/linux/ubuntu hardy/
>>>
>>> The address could/should be a different mirror, but there needs to
be
>>> a cran mirror in you list somewhere.
>>>
>>> Michael
>>>
>>> Agustin Lobo wrote:
>>>> Michael:
>>>>
>>>> I do have the backports activated. This is the entry in my 
>>>> sources.list:
>>>> deb http://archive.ubuntu.com/ubuntu/ hardy-backports
restricted
>>>> main multiverse universe
>>>> deb-src http://archive.ubuntu.com/ubuntu/ hardy-backports
restricted
>>>> main multiverse universe
>>>>
>>>> And this is the output to what you suggested.
>>>>
>>>> root at alobo-laptop:/home/alobo# dpkg --get-selections | grep
r-base
>>>> r-base-core                    install
>>>> r-base-dev                    install
>>>> r-base-html                    install
>>>> root at alobo-laptop:/home/alobo# dpkg --get-selections | grep
r-cran
>>>> r-cran-abind                    deinstall
>>>> r-cran-boot                    install
>>>> r-cran-cluster                    install
>>>> r-cran-codetools                install
>>>> r-cran-effects                    deinstall
>>>> r-cran-foreign                    install
>>>> r-cran-kernsmooth                install
>>>> r-cran-lattice                    install
>>>> r-cran-matrix                    install
>>>> r-cran-mgcv                    install
>>>> r-cran-nlme                    install
>>>> r-cran-relimp                    deinstall
>>>> r-cran-robustbase                install
>>>> r-cran-rpart                    install
>>>> r-cran-survival                    install
>>>> r-cran-vr                    install
>>>>
>>>> My system is uptodate, I regularly install what I'm told by
Update
>>>> Manager.
>>>>
>>>> I'm going to uninstall and install back r-base from
Synaptic.
>>>> If I keep having the same problem afterwards, do you expect
>>>> that installing everything from sources could solve the
problem?
>>>> Will it be hard ?
>>>> How much time should I pre-allocate?
>>>>
>>>> Thanks
>>>>
>>>> Agus
>>>>
>>>>
>>>>
>>>>
>>>> Michael Rutter wrote:
>>>>> Agus,
>>>>>
>>>>> robustbase just installed fine on my stock 8.04 system. 
Please
>>>>> make sure that you have added all the repositories and
packages
>>>>> suggested on this page:
>>>>>
>>>>> http://cran.r-project.org/bin/linux/ubuntu/
>>>>>
>>>>> Backports are important, and make sure you have r-base-dev
>>>>> installed.  You may also need to be root (via sudo) to
install,
>>>>> although there are instructions for local installation. 
You can
>>>>> run the following commands to see what R related packages
you have
>>>>> installed.
>>>>>
>>>>> dpkg --get-selections | grep r-base
>>>>> dpkg --get-selections | grep r-cran
>>>>>
>>>>> Michael
>>>>>
>>>>
>>>
>>
>